title: The oncofusion protein FUS-ERG targets key hematopoietic regulators and modulates the all-trans retinoic acid signaling pathway in t(16;21) acute myeloid leukemia

status: Public on Jun 23 2015

first: Joost

last: Martens

state: Nederland

department: RIMLS

institute: Radboud University

summary: Fusion proteins involving the ETS factor ERG have been associated with multiple cancers such as Ewing's sarcoma and prostate cancer. In acute myeloid leukemias harboring  t(16;21) another ERG fusion protein is expressed, FUS-ERG. Here, we found that this FUS-ERG oncofusion protein acts in the context of a heptad of proteins (ERG, FLI1, GATA2, LYL1, LNMO2, RUNX1 and TAL1) central to proper expression of genes involved in maintaining a stem cell hematopoietic phenotype. Moreover, in t(16;21) FUS-ERG co-occupies genomic regions bound by the nuclear receptor heterodimer RXR-RARA inhibiting target gene expression and interfering with hematopoietic differentiation. All-Trans Retinoic Acid treatment of t(16;21) cells as well as FUS-ERG knock down alleviate the myeloid differentiation block. Together, the results suggest that FUS-ERG acts as a transcriptional repressor of the retinoic acid signaling pathway.

overall_design: Cell lines were used for RNA extraction for RNA-seq and ChIP experiments for ChIP-seq.

first: Ana

last: Sotoca

first: Koen

last: Prange

first: Bob

last: Reijnders

first: Amit

last: Mandoli

first: Luan

middle: N

last: Nguyen

first: Hendrik

last: Stunnenberg

middle: H


title: Tead2 expression levels control the subcellular distribution of Yap and Taz, zyxin expression and epithelial-mesenchymal transition (expression)

status: Public on Mar 12 2014

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

summary:
Cellular changes during an epithelial-mesenchymal transition (EMT) largely rely on global changes in gene expression orchestrated by transcription factors.
Tead transcription factors and their co-factors Yap and Taz have been shown to be implicated in EMT, nevertheless, their direct and indirect target genes during EMT have remained elusive.
We used microarrays to detail the changes in global programme of gene expression during TGFβ-induced EMT in a murine breast cancer cell line (Py2T).

overall_design: We compared expression profiles of treated Py2T breast cancer cell lines (5 days of TGFβ treatment 2ng/ml) to profiles of untreated cells, we used 2 biological replicates for each condition.

first: Maren

last: Diepenbruck

first: Lorenz

last: Waldmeier

first: Robert

last: Ivanek

first: Gerhard

last: Christofori


title: Attenuated sensing of SHH underlies adaptive evolution of bovine limbs

status: Public on Jun 19 2014

summary: Artiodactyls display skeletal adaptations for cursorial (running) locomotion. In these animals, the distal limb skeleton is symmetric, which facilitates walking on the tips of the two central digits, while lateral digits are reduced or lost. We have identified that one primary molecular alteration during the formation of the bovine limb is that, in contrast to mouse, the posterior limb bud mesenchyme does not upregulate Ptch1 expression in response to SHH. We have tracked down this dissimilarity to a cis-regulatory SHH-responsive element that is functionally altered in bovine and established a causal link between lack of upregulation of Ptch1 and acquisition of a symmetric distal autopod.

overall_design: A high resolution 4C-seq protocol involving two restriction digests was applied to viewpoint in Ptch1 promoter (mm9 chr13:63,667,995-63,669,157) in three different tissues, allowing robust detection of physical interactions between regulatory DNA elements.

first: Javier

last: Lopez-Rios

first: Amandine

last: Duchesne

first: Rolf

last: Zeller


title: Tead2 expression levels control the subcellular distribution of Yap and Taz, zyxin expression and epithelial-mesenchymal transition (ChIP-seq)

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Cellular changes during an epithelial-mesenchymal transition (EMT) largely rely on global changes in gene expression orchestrated by transcription factors. Tead transcription factors and their co-factors Yap and Taz have been shown to be implicated in EMT, nevertheless, their direct target genes during EMT have remained elusive.We used genome-wide chromatin immunoprecipitation and next generation sequencing to identify diect Tead2 target genes during EMT.

overall_design: Py2T cells (murine breast cancer cell line) were treated with TGFβ for 5 days and subjected to ChIP using an antibody for Tead2 followed by next generation sequencing (Illumina HiSeq 2000; n=2)


title: Dissecting the signalling pathways underlying cellular senescence

status: Public on Jan 21 2011

city: London

first: Parmjit

last: Jat

address: Queen Square

department: Institute of Neurology

country: United Kingdom

institute: UCL

summary: Cellular senescence is a program of irreversible cell cycle arrest that normal cells undergo in response to progressive shortening of telomeres, changes in telomeric structure, oncogene activation or oxidative stress.  The underlying signalling pathways, potentially of major clinicopathological relevance, are unknown.  A major stumbling block to studying senescence has been the absence of suitable model systems because of the asynchrony of this process in heterogeneous cell populations. To simplify this process many investigators study oncogene-induced senescence due to expression of activated oncogenes where senescence occurs prematurely without telomere attrition and can be induced acutely in a variety of cell types. We have taken a different approach by making use of the finding that reconstitution of telomerase activity by introduction of the catalytic subunit of human telomerase alone is incapable of immortalising all human somatic cells, but inactivation of the p16-pRB and p53-p21 pathways are required in addition.  The ability of SV40 large T antigen to inactivate the p16-pRB and p53-p21 pathways has enabled us to use a thermolabile mutant of LT antigen, in conjunction with hTERT, to develop conditionally immortalised human (HMF3A) fibroblasts that are immortal but undergo an irreversible growth arrest when the thermolabile LT antigen is inactivated leading to activation of pRB and p53. When these cells cease dividing, senescence-associated- b-galactosidase activity is induced and the growth-arrested cells have morphological features and express genes in common with senescent cells.  Since these cells growth arrest in a synchronous manner they are an excellent starting point for dissecting the pathways that underlie cellular senescence and act downstream of p16-pRB and p53-p21 pathways.      We have combined genome-wide expression profiling with genetic complementation to undertake identification of genes that are differentially expressed when these conditionally immortalised human fibroblasts undergo senescence upon activation of the p16-pRB and p53-p21 tumour suppressor pathways.

overall_design: Genes differentially expressed upon senescence will be identified by comparing arrays from growing versus senescent cells. Changes in gene expression due to the temperature shift will be eliminated by comparing with array data from the non-conditional HMF3S cells grown at 34°C ±0.5°C and 38°C ±0.5°C.  To determine if the changes in gene expression upon senescence are specific and reversible, the set of differential genes will then be overlaid with array data from cells in which senescence has been bypassed by inactivation of the p16-pRB and p53-p21 tumour suppressor pathways

first: Jat

last: Parmjit

first: Rovillain

last: Emilie

first: Hummerich

last: Holger

first: Mansfield

last: Louise